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enola-dkfzenola-dkfz
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fixed one sided between for dates
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+266
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4 files changed

+266
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‎resources/test/result_after.cql‎

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library Retrieve
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using FHIR version '4.0.0'
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include FHIRHelpers version '4.0.0'
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codesystem icd10: 'http://hl7.org/fhir/sid/icd-10'
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codesystem SampleMaterialType: 'https://fhir.bbmri.de/CodeSystem/SampleMaterialType'
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context Patient
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define AgeClass:
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if (Patient.birthDate is null) then 'unknown' else ToString((AgeInYears() div 10) * 10)
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define Gender:
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if (Patient.gender is null) then 'unknown' else Patient.gender
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define Custodian:
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First(from Specimen.extension E
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where E.url = 'https://fhir.bbmri.de/StructureDefinition/Custodian'
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return (E.value as Reference).identifier.value)
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define function SampleType(specimen FHIR.Specimen):
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case FHIRHelpers.ToCode(specimen.type.coding.where(system = 'https://fhir.bbmri.de/CodeSystem/SampleMaterialType').first())
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when Code 'plasma-edta' from SampleMaterialType then 'blood-plasma'
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when Code 'plasma-citrat' from SampleMaterialType then 'blood-plasma'
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when Code 'plasma-heparin' from SampleMaterialType then 'blood-plasma'
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when Code 'plasma-cell-free' from SampleMaterialType then 'blood-plasma'
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when Code 'plasma-other' from SampleMaterialType then 'blood-plasma'
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when Code 'plasma' from SampleMaterialType then 'blood-plasma'
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when Code 'tissue-formalin' from SampleMaterialType then 'tissue-ffpe'
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when Code 'tumor-tissue-ffpe' from SampleMaterialType then 'tissue-ffpe'
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when Code 'normal-tissue-ffpe' from SampleMaterialType then 'tissue-ffpe'
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when Code 'other-tissue-ffpe' from SampleMaterialType then 'tissue-ffpe'
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when Code 'tumor-tissue-frozen' from SampleMaterialType then 'tissue-frozen'
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when Code 'normal-tissue-frozen' from SampleMaterialType then 'tissue-frozen'
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when Code 'other-tissue-frozen' from SampleMaterialType then 'tissue-frozen'
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when Code 'tissue-paxgene-or-else' from SampleMaterialType then 'tissue-other'
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when Code 'derivative' from SampleMaterialType then 'derivative-other'
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when Code 'liquid' from SampleMaterialType then 'liquid-other'
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when Code 'tissue' from SampleMaterialType then 'tissue-other'
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when Code 'serum' from SampleMaterialType then 'blood-serum'
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when Code 'cf-dna' from SampleMaterialType then 'dna'
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when Code 'g-dna' from SampleMaterialType then 'dna'
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when Code 'blood-plasma' from SampleMaterialType then 'blood-plasma'
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when Code 'tissue-ffpe' from SampleMaterialType then 'tissue-ffpe'
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when Code 'tissue-frozen' from SampleMaterialType then 'tissue-frozen'
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when Code 'tissue-other' from SampleMaterialType then 'tissue-other'
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when Code 'derivative-other' from SampleMaterialType then 'derivative-other'
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when Code 'liquid-other' from SampleMaterialType then 'liquid-other'
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when Code 'blood-serum' from SampleMaterialType then 'blood-serum'
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when Code 'dna' from SampleMaterialType then 'dna'
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when Code 'buffy-coat' from SampleMaterialType then 'buffy-coat'
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when Code 'urine' from SampleMaterialType then 'urine'
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when Code 'ascites' from SampleMaterialType then 'ascites'
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when Code 'saliva' from SampleMaterialType then 'saliva'
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when Code 'csf-liquor' from SampleMaterialType then 'csf-liquor'
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when Code 'bone-marrow' from SampleMaterialType then 'bone-marrow'
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when Code 'peripheral-blood-cells-vital' from SampleMaterialType then 'peripheral-blood-cells-vital'
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when Code 'stool-faeces' from SampleMaterialType then 'stool-faeces'
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when Code 'rna' from SampleMaterialType then 'rna'
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when Code 'whole-blood' from SampleMaterialType then 'whole-blood'
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when Code 'swab' from SampleMaterialType then 'swab'
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when Code 'dried-whole-blood' from SampleMaterialType then 'dried-whole-blood'
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when null then 'Unknown'
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else 'Unknown'
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end
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define Specimen:
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if InInitialPopulation then [Specimen] S where (((((FHIRHelpers.ToDateTime(S.collection.collected) >= @2015-01-01) )))) else {} as List<Specimen>
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define Diagnosis:
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if InInitialPopulation then [Condition] else {} as List<Condition>
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define function DiagnosisCode(condition FHIR.Condition):
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condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()
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define function DiagnosisCode(condition FHIR.Condition, specimen FHIR.Specimen):
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Coalesce(
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condition.code.coding.where(system = 'http://hl7.org/fhir/sid/icd-10').code.first(),
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condition.code.coding.where(system = 'http://fhir.de/CodeSystem/dimdi/icd-10-gm').code.first(),
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condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first(),
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specimen.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code.first()
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)
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define InInitialPopulation:
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((((exists from [Specimen] S
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where FHIRHelpers.ToDateTime(S.collection.collected) >= @2015-01-01 ))))

‎resources/test/result_before.cql‎

Lines changed: 86 additions & 0 deletions
Original file line numberDiff line numberDiff line change
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library Retrieve
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using FHIR version '4.0.0'
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include FHIRHelpers version '4.0.0'
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codesystem icd10: 'http://hl7.org/fhir/sid/icd-10'
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codesystem SampleMaterialType: 'https://fhir.bbmri.de/CodeSystem/SampleMaterialType'
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context Patient
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define AgeClass:
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if (Patient.birthDate is null) then 'unknown' else ToString((AgeInYears() div 10) * 10)
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define Gender:
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if (Patient.gender is null) then 'unknown' else Patient.gender
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define Custodian:
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First(from Specimen.extension E
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where E.url = 'https://fhir.bbmri.de/StructureDefinition/Custodian'
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return (E.value as Reference).identifier.value)
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define function SampleType(specimen FHIR.Specimen):
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case FHIRHelpers.ToCode(specimen.type.coding.where(system = 'https://fhir.bbmri.de/CodeSystem/SampleMaterialType').first())
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when Code 'plasma-edta' from SampleMaterialType then 'blood-plasma'
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when Code 'plasma-citrat' from SampleMaterialType then 'blood-plasma'
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when Code 'plasma-heparin' from SampleMaterialType then 'blood-plasma'
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when Code 'plasma-cell-free' from SampleMaterialType then 'blood-plasma'
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when Code 'plasma-other' from SampleMaterialType then 'blood-plasma'
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when Code 'plasma' from SampleMaterialType then 'blood-plasma'
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when Code 'tissue-formalin' from SampleMaterialType then 'tissue-ffpe'
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when Code 'tumor-tissue-ffpe' from SampleMaterialType then 'tissue-ffpe'
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when Code 'normal-tissue-ffpe' from SampleMaterialType then 'tissue-ffpe'
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when Code 'other-tissue-ffpe' from SampleMaterialType then 'tissue-ffpe'
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when Code 'tumor-tissue-frozen' from SampleMaterialType then 'tissue-frozen'
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when Code 'normal-tissue-frozen' from SampleMaterialType then 'tissue-frozen'
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when Code 'other-tissue-frozen' from SampleMaterialType then 'tissue-frozen'
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when Code 'tissue-paxgene-or-else' from SampleMaterialType then 'tissue-other'
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when Code 'derivative' from SampleMaterialType then 'derivative-other'
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when Code 'liquid' from SampleMaterialType then 'liquid-other'
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when Code 'tissue' from SampleMaterialType then 'tissue-other'
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when Code 'serum' from SampleMaterialType then 'blood-serum'
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when Code 'cf-dna' from SampleMaterialType then 'dna'
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when Code 'g-dna' from SampleMaterialType then 'dna'
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when Code 'blood-plasma' from SampleMaterialType then 'blood-plasma'
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when Code 'tissue-ffpe' from SampleMaterialType then 'tissue-ffpe'
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when Code 'tissue-frozen' from SampleMaterialType then 'tissue-frozen'
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when Code 'tissue-other' from SampleMaterialType then 'tissue-other'
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when Code 'derivative-other' from SampleMaterialType then 'derivative-other'
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when Code 'liquid-other' from SampleMaterialType then 'liquid-other'
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when Code 'blood-serum' from SampleMaterialType then 'blood-serum'
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when Code 'dna' from SampleMaterialType then 'dna'
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when Code 'buffy-coat' from SampleMaterialType then 'buffy-coat'
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when Code 'urine' from SampleMaterialType then 'urine'
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when Code 'ascites' from SampleMaterialType then 'ascites'
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when Code 'saliva' from SampleMaterialType then 'saliva'
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when Code 'csf-liquor' from SampleMaterialType then 'csf-liquor'
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when Code 'bone-marrow' from SampleMaterialType then 'bone-marrow'
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when Code 'peripheral-blood-cells-vital' from SampleMaterialType then 'peripheral-blood-cells-vital'
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when Code 'stool-faeces' from SampleMaterialType then 'stool-faeces'
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when Code 'rna' from SampleMaterialType then 'rna'
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when Code 'whole-blood' from SampleMaterialType then 'whole-blood'
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when Code 'swab' from SampleMaterialType then 'swab'
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when Code 'dried-whole-blood' from SampleMaterialType then 'dried-whole-blood'
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when null then 'Unknown'
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else 'Unknown'
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end
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define Specimen:
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if InInitialPopulation then [Specimen] S where (((((FHIRHelpers.ToDateTime(S.collection.collected) <= @2015-01-01) )))) else {} as List<Specimen>
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define Diagnosis:
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if InInitialPopulation then [Condition] else {} as List<Condition>
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define function DiagnosisCode(condition FHIR.Condition):
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condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first()
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define function DiagnosisCode(condition FHIR.Condition, specimen FHIR.Specimen):
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Coalesce(
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condition.code.coding.where(system = 'http://hl7.org/fhir/sid/icd-10').code.first(),
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condition.code.coding.where(system = 'http://fhir.de/CodeSystem/dimdi/icd-10-gm').code.first(),
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condition.code.coding.where(system = 'http://fhir.de/CodeSystem/bfarm/icd-10-gm').code.first(),
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specimen.extension.where(url='https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis').value.coding.code.first()
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)
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define InInitialPopulation:
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((((exists from [Specimen] S
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where FHIRHelpers.ToDateTime(S.collection.collected) <= @2015-01-01 ))))

‎src/ast.rs‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -44,8 +44,8 @@ pub struct NumRange {
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#[derive(Serialize, Deserialize, Debug, Clone)]
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pub struct DateRange {
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pub min: String, // we don't parse dates yet
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pub max: String,
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pub min: Option<String>, // we don't parse dates yet
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pub max: Option<String>,
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}
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#[derive(Serialize, Deserialize, Debug, Clone)]

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